That must be the problem. Take note that in the pdb
file, the a.a. residues have a chain identifier as
well while the cofactor has none.
kind regards,
jonathan
--- Roberto Sanchez <> skrev:
> Hi,
>
> Try explicit naming of the residue numbers in the
> structureX line of the
> .ali file (including the FAD residue).
>
> Best,
>
> Roberto
>
> --
> Roberto Sanchez, Assistant Professor
> Structural Biology Program, Department of Physiology
> & Biophysics and
> Institute for Computational Biomedicine, Mount Sinai
> School of Medicine
> Box 1677, 1425 Madison Avenue, New York, NY 10029
> phone +1 (212) 659 8648, fax +1 (212) 849 2456
> http://physbio.mssm.edu/~sanchez/
>
> > -----Original Message-----
> > From:
> >
>
[]On">mailto:]On
> Behalf Of Ralf
> > Schmid
> > Sent: Tuesday, September 24, 2002 6:29 AM
> > To:
> > Subject: HETATM_IO
> >
> >
> >
> > Dear all,
> >
> >
> > I'm trying to model a protein including a
> cofactor, but get an error
> > message pointing towards problems in the alignment
> and/or pdb file.
> > Modelling without cofactor (i.e. removing "/."
> from the alignment file)
> > works fine. I can't figure out what causes the
> problem.
> >
> > Any help will be appreciated, please see the files
> below.
> >
> > Thanks in advance,
> >
> > ralf
> >
> >
> > xxx.log:
> > <snip>
> > TOP_________> 120 106 READ_ALIGNMENT FILE =
> ALNFILE, ALIGN_CODES = KNOWNS
> > SEQUE;
> > NCE
> > Dynamically allocated memory at amaxseq
> [B,kB,MB]:
> > 2205269 2153.583 2.103
> > openf5__224_> Open 11 OLD SEQUENTIAL xxx.ali
> > openf5__224_> Open 13 OLD SEQUENTIAL ./yyy.pdb
> > Dynamically allocated memory at amaxbnd
> [B,kB,MB]:
> > 9440821 9219.552 9.003
> > openf5__224_> Open 11 OLD SEQUENTIAL xxx.ali
> > openf5__224_> Open 13 OLD SEQUENTIAL ./yyy.pdb
> > rdpir___648E> Alignment sequence not found in PDB
> file: 1 ./yyy.pdb
> > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
> >
> >
> > xxx.top:
> > INCLUDE
> > SET OUTPUT_CONTROL= 1 1 1 1 1
> > SET ALNFILE = 'xxx.ali'
> > SET KNOWNS = 'yyy'
> > SET SEQUENCE = 'xxx'
> > SET STARTING_MODEL = 20
> > SET ENDING_MODEL = 20
> > SET HETATM_IO = on
> > CALL ROUTINE = 'model'
> >
> >
> > xxx.ali:
> > >P1;xxx
> > sequence:xxx:.:.:.:.:.:.:.:.
> > VKNER/.*
> > >P1;yyy
> > structureX:yyy:.:.:.:.:.:.:.:.
> > VKQER/.*
> >
> >
> > yyy.pdb:
> > <snip>
> > ATOM 3488 OXT ARG A 447 31.403 66.404
> 103.394 1.00 65.84 O
> > TER 3489 ARG A 447
> > HETATM 3490 AP FAD 448 60.780 56.948
> 67.003 1.00 33.65 P
> > <snip>
> >
> >
> >
> >
>
-----------------------------------------------------------------
> > Dr. Ralf Schmid
> > ICMB
> > The University of Edinburgh
> > Michael Swann Building 3.14
> >
>
-----------------------------------------------------------------
> >
> >
> >
> >
>
>
=====
Jonathan LS Esguerra
Structural Chemistry
Department of Medical Biochemistry
Gothenburg University, Sweden
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